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503 Cards in this Set
- Front
- Back
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Genetic code
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Set of rules for transforming nucleotides to AAs
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chromatin, what, classification
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complex of DNA and protein that makes up chromosomes, euchromatin (extended and) and heterochomatin (condensed)
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protein synthesis starts w which end
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N-terminus
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splicing, performed by
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snRNPs (small ribonuclear proteins) making spliceosomes, self-splicing introns
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CpG islands, length, found where
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300-3000 bps, in/near (70%) of human promoters
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RNA interference
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intranuclear system that help to control activity of genes by binding to RNAs, micro RNA (mRNA) and small interfering RNA (siRNA)
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repressor, what, coded by
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DNA-binding protein that repress expression of proteins during transcription, regulator genes
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RNA polymerase III, transcribe what
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5S rRNA, tRNA, other small RNAs
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DNA-binding domain (DBD)
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protein domain which contains a motif that can bind to DNA
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TATA box
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DNA sequence found in promoter region of most genes in eukaryotes and archea (considered to be the core promoter sequence, binding site of transcription factors, histones, and RNA polymerase)
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start codon
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AUG, produce Met in eukaryotes and fMet in prokaryotes
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# of reading frames in dsDNA
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6 (3 on each strand), (overlapping genes, used by viruses)
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initiation factor
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proteins that bind to the small subunit of the ribosome during initiation of translation
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5' cap
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a methylated guanine nucleotide added to the 5' end of eukaryotic mRNA, necessary to initiate translation of mRNA
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allosteric molecules
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molecule can exist in two or more differing conformations
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allosteric regulation
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allosteric changes in protein conformation produced by one ligand affect the binding of a second ligand, u multimeric proteins
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elaunin, what, found where
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immature elastic fiber, small deposition of elastin in oxytalan, found in CT of dermis (esp w sweat glands)
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functional types of protein
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1 structural 2 enzymes 3 motor 4 transport 5 storage 6 signaling 7 receptor 8 regulatory 9 antibodies 10 other proteins w special function (GPF - green fluorescent protein)
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genus
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a group of species exhibiting similar characteristics
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lamellipodia
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cell protrusion (flattened) supported by meshwork of actin filaments, which is extended at the leading edge of a crawling animal cell
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mechanism of protein activity regulation
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1 binding of ion 2 binding of small molecule (retinal in rhodopsin) 3 phosphorylation 4 binding of GTP 5 proteolytic cleavage (insulin)
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motor proteins
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1 myosin 2 dynein 3 kinesin
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oxytalan, what, found where
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immature form of elastic fiber, m composed of microfibrillar units (fibrillin), found in periodontal ligaments and gingivae
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proteasomes only degrade proteins marked for degradation by
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ubiquitin
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proteins can be degraded in
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1 proteasomes 2 lysosomes 3 extracellularly
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regulatory proteins, what? ie
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regulate function of other proteins or macromolecules by binding to them 1 chaperons 2 cyclins 3 transcription facotrs
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secondary structure, types
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1 alpha-helix (side-chains out) 2 beta-sheet (side chain above and below plane) 3 beta-turn (u gly, pro)
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storage proteins
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1 casein 2 ferritin 3 ovalbumin (storage of AAs for embryo)
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transport proteins
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1 Hb 2 transferrin 3 albumin
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bacillus, types, ie
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1 bacillus (e coli, salmonella) 2 coccobacillus 3 diplobacillus 4 streptobacillus (line)
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bacteria vs archaea
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1 no nucleosome, nucleosom-ish 2 no introns, tRNA and rRNA have intron 3 peptidoglycan cell wall, pseudopeptidoglycan cell wall
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cocci (''berry''), types - shape, ie
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1 cocci 2 diplococci 3 streptococci (form line) 4 staphylococci (form cluster)
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difference between eukaryotic and prokaryotic flagella
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prokaryotic flagella has no internal fibrils (composed of flagellin), don't flex and source of energy is not ATP
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functional characteristics of prokaryotic genome (replication, transcription, haploid/diploid, introns and exons?)
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1 1 replicon 2 operons 3 haploid 4 only exons (5 asexual reproduction)
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gram+ bacteria, cell wall from? epitope?
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only peptidoglycan polymers, teichoic acid
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gram- bacteria, structure of cell wall?
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peptidoglycan polymers and outer membrane (lipopolysaccharide coat, lipopolysaccharide porins, prominent periplasmic space (above plasma membrane))
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how to differentiate gram+ and gram-?
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in gram-, fat-soluble color complex (iodine-based) is washed out by decolorizer from outer lipid layer, in gram+ it remains (in the peptidoglycan)
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important factor explaining rapid proliferation of prokaryotes
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replication can start again from the replicon (the entire chromosome is a replicon) before the first replication is finished
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nucleoid, where, genotype, proteins, # of genes
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1 nuclear region 2 1 molecule of dsDNA and protein 3 DNA is u circular, loop-formed attached to plasma membrane 4 histone-like proteins (HLP) 4 1000-4000 genes
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proacaryotes vs eukaryotes
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1 1-10 um, 5-150 um 2 1k-4k genes, 10k-30k genes 3 no nucleus, nucleus 4 non-mitotic division (binary fission), mitotic 5 not seperated transcription and translation, separated 6 70s ribosomes, 80s ribosomes 7 no cytoskeleton, cytoskeleton 8 no organelles, organelles
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prokaryotic cell wall, structure
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polymers of peptidoglycan (murein) = (N-acetylglucosamine+n-acetylmuramic acid), linked by short peptide chains
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shapes of procaryotic cells
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1 cocci (shperical) 2 bacillus (rod-shaped) 3 spiral (spirillum, vibrio, spirochete)
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where is respiratory chain enzymes and enzymes of photosynthesis in prokaryotes located?
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in cytoplasmic membrane
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why do we supoose that mitochondria have an procaryotic origin
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1 70s ribosomes 2 circular DNA
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actin, associated w which energy compound, at which ends
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ATP, ATP at +/polymerization/growth end, ADP at -/depolymerization end
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centrosome/cytocentrum
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a zone of cytoplasm containing two centrioles - u located near the nucleus
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intermediate filaments, physical characteristic
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rope-like
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microfilaments, physical characteristic
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flexible
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microtubule organizing center (MTOC)
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place in cells from which most microtubules radiate, in the center of this center is the centriole
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microtubule, function
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1 mitotic spindle (centrosome = 2x centriole), aster MT, polar MT, kinetochore MT 2 cilia+flagella (- end in basal body, dynein-mediated) 3 intracellular tracks
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microtubule, physical characteristic
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rigid
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microtubules, polymerization
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GTP, +/growth end - highest affinity for GTP, -/depolymerizing end - highest affinity to GDP (attached to MTOC)
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microtubules, structure
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Alpha+beta tubulin dimer -> protofilament (polymer) -> 13 protofilaments -> microtubule (hollow)
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motor proteins on intercellular tracks of microtubules
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dynein - toward - end, kinesin - toward + end
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Penicillin, mechanism
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bind and inhibit transpeptidase = no cross-linking of peptidoglycan chain = osmotic lysis
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Rifampicin, mechanism
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inhibit bacterial RNA polymerase
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structure of microfilaments
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from monomer of actin, form a two-stranded helix
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tetracyclin and streptomycin, mechanism
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inhibit translation
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central dogma of molecular biology
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DNA (can replicate itself) to RNA to protein, e = replication of RNA, RT
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DNA double helix, structural characteristics
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right-handed, antiparallel strands
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DNA tautomerism, most common, pair w what
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C, pair w A (not detected by proofreading)
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eucaryote, DNA polymerase alpha
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synthesis of lagging strand (I in prokaryotes)
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Eukaroytes, DNA polymerase gamma
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mitochondrial DNA
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eukaryotes, DNA polymerase beta and epsilon
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DNA repair
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eukaryotes, DNA polymerase delta
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synthesis of leading strand (III in prokaryotes)
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replicon in eucaryotes
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10 000..
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why does DNA polymerase work in 5' to 3' direction?
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so it can proofread, the incoming nucleotide brings the energy(5'), if the strand brought the energy, it would not be possible to elongate a proof-read fixed/cut off strand
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AA is attached to which end of the tRNA?
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3'
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aminoacyl-tRNA synthetase catalyze
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AA + ATP = aminoacyl-AMP, aminoacyl-AMP + tRNA = aminoacyl-tRNA
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anticodon
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the trinucleotide sequence complementary to a codon of a mRNA found in the tRNA
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coding strand of DNA
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the non-templating strand
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error in eukaryotic replication machinery? combined w mismatch repair system?
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1/107, 1/109
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function of poly-A tail and rna capping of mRNA
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1 increase stability 2 aid its export 3 indicator for protein-synthesis machinery that bonds ends are present, = message complete
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how can 20 AAs be fitted to 61 codons?
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through wobble-base pairing (3rd nucleotide of codon can be mismatched)
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number of aminoacyl-tRNA synthetase
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20
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number of nucleotide triplets
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64 (4 x 4 x 4)
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picornavirus, types
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1 poliovirus (infantile paralysis/poliomyelitis) 2 hep A 3 rhinovirus
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retroviruses
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1 HIV-1 2 HTLV (human T-cell lymphotropic virus) 3 rous sarcoma v (affect animals)
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RNA capping
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at 5' end of mRNA, 7-methylguanine is attached via 5' to 5' linkage
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RNA polymerase, error frequency
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1/104
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role of RNA in snRNPs
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recognize and pair with nucleotide sequence that mark beginning and end of each intron
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UV radiation produce which change in DNA
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dimers = 1 thymidine dimer 2 C-G (pyrimidine dimer)
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alternative promoters - function
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can result in tissue-specific expression patterns (dystrophin gene have 7 tissue-specific promoters)
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cis-acting element
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acting from the same molecule, ie regulatory DNA sequence
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combinatorial control of gene transcription refer to
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combined effect of several regulatory proteins (activator and repressor) working together to control the expression of a single gene
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difference between general transcription factors and gene regulatory proteins (activators, repressors)
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general transcription factors - large set of proteins, for all types of genes, assemble at promoter (TATA box, CpG islands), gene regulatory proteins - can regulate individual genes, can bind to a regulatory sequence far away from the promoter (activator bind to enhancer, repressor bind to silencer)
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DNA methylation, by which enzyme, does what
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DNA methyltransferase, catalyze addition of methyl group to cytosine (5-methylcytosine)
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enzyme that create peptide bond in ribosome
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peptidyl transferase (rRNA)
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how does the stop codons UAA, UGA and UAG mediate termination of translation?
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release factors bind to the stop codons and make the peptidyl transferase add water instead of AA
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levels of regulation of gene expression
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1 genome (DNA) 2 transcription (DNA to primary transcript) 3 posttranscriptional modifications (primary transcript to mRNA) 4 translation (lifetime of mRNA, mRNA-binding proteins (IRP) 5 posttranslational modifications 6 protein degradation
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most common monosaccharides to add to proteins
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1 n-acetylglucosamine 2 mannose 3 glucose 4 galactose 5 n-acetylneuraminic acid (NAMA)
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number of human proteins
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more than 150 000
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posttranscriptional modifications
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1 RNA capping and polyadenylation 2 alternative splicing 3 RNA editing (insertion, deletion or substitutions (A to I, C to U) of nucleotides into transcribed RNA, enzyme-mediated)
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posttranslational modification, types
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1 removal of met from N-terminal 2 removal of signal sequence 3 proteolytic cleavage (insulin) 4 cystine formation 5 chemical modification of AAs (+ Pi, +OH, +sugar, +prosthetic group)
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regulation of gene expression at genome level
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1 gene amplification 2 genome rearrangement (transposons, Ig) 3 eu/heterochromatin (histone acetylation) 4 DNA methylation
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trans-acting element
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acting from a different molecule, ie protein to DNA
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why is tRNA w AUG special
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start codon, only that bind to P site of ribosome
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connexon
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half a gap junction, hexamer of connexin, transport molecules up to 1 kDa
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DNA-binding motifs
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1 Homeodomain 2 Zinc finger (contain a Zn) 3 Leucine zipper 4 The helix-loop-helix motif (HLH) (u form dimer) 5 Helix-turn-helix motif (u form dimer)
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fibronectin, how many subunits
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2 - dimer
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functional types of cell junctions
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1 occluding cell junctions 2 anchoring cell junctions 3 communicating cell junctions
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GAGs
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1 hyaluronan 2 chondroitin sulphate 3 heparan sulphate 4 keratan sulphate
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gas signal molecules, mechanism
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1 diffuse 2 interact w relevant enzyme (ie CO interact w guanylyl cyclase)
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Helix-loop-helix motif (HLH)
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DNA-binding motif of protein, 1 short alpha helix connected to a longer by a loop, u involved in dimerization of subunits of a protein (found in c-myc)
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hyaluronan, characteristics
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simplest GAG which don't contain sulphate group, and form aggregating portion of a proteoglycan complex
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hydrophobic signaling molecules - mechanism
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1 Diffuse 2 complex w intracellular receptor 3 complex bind to DNA 4 regulate gene expression
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hydrophobic signaling molecules, ie
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1 steroid hormones 2 thyroid hormones 3 retinoids 4 vitamin D
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Leuzine zipper
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a structural DNA-bindint motif, in which leucyl residues along one edge of a alpha helix can interdigitate w a similar structure on another protein - forming a dimer
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part of a protein domain that can bind to ie DNA
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motif
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sigma factor
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subunit of RNA polymerase of prokaryotes, the more similar the promoter is to the sigma subunit, the more frequent is the transcription of it
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signaling molecules
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1 proteins/peptides 2 low-molecular weights (AAs, NAs, steroids, retinoids, FA-derivatives) 3 gases (NO, CO)
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alpha subunit of G protein can activate
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1 phospholipase C (Gq) 2 adenylyl cyclase (Gs) 3 cGMP phosphodiesterase (Gt) (Gi - inhibit adenylyl cyclase)
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anti-inflammatory action of ibuprofen and aspirin?
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inhibit prostaglandin synthesis (ie from DAG)
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DAG, produced by? location? effect?
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PLC form PIP2, remain bound to membrane, activate protein kinase C, substrate for prostaglandin synthesis
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G protein linked receptor - mechanism
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1 receptor+ligand 2 substitute bound GDP on alpha of G protein w GTP 3 alpha is released 4 alpha activates other proteins (inactivated when GTP is hydrolyzed to GDP)
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G-protein linked receptor, structure
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7 transmembrane alpha helix, G protein has 3 parts - alpha, beta, gamma
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IP3, receptors?
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IP3-gated Ca2+ channels in ER membrane (Ca2+ activate PKC)
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Nitric oxide (NO) is produced by, from which enzyme, by which reaction
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arginine, NO synthase, deamination
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PKC, phosphorylate which residues
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serine, threonine
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receptor desensitization
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a prolonged exposure to a stimulus decreases the cells' response to that level of the stimulus, mechanisms = 1 receptor seuqestration (endocyte and recycle) 2 receptor-down regulation 3 receptor inactivation 4 inactivation of signaling protein 5 production of inhibitory protein (3-5 via negative feedback mechanisms)
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receptor down-regulation
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1 receptor internalization (endocytosis, clathrin-coated pits) followed by degradation (involved in down-regulation w drugs, medicine..)
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receptor types
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1 ion channel-linked R (neurotransmitters, IP3) 2 protein-kinase linked R (a intrinsic kinase activity/receptor kinases, R associated w kinases) 3 G protein-linked R
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receptors activating phospholipase C (PLC) (Gq)
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1 5HT2 serotonergic R 2 alpha1 adrenergic R 3 calcitonin R 4 H1 histamine R
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adenylyl cyclase, activated by which receptors
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1 beta-adrenergic Rs 2 TSH Rs
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adenylyl cyclase, structure, mechanism/do
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transmembrane enzyme, produce cAMP from ATP (cAMP is degraded by cAMP phosphodiesterase to AMP), cAMP activate PKA
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cGMP phosphodiesterase, mechanism
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1 photon 2 activate rhodopsin (11-cis retinal to trans retinal = change in protein (opsin)) 3 activate G protein (Gt, t= transducin) 4 activate cGMP phosphodiesterase 5↓cGMP 6 close channels (cGMP+gated cation channels) 7 inhibit synaptic signaling
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CREB protein, full name, mechanism/do
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cAMP response element-binding protein, transcription factor for CRE (cAMP response element), CRE is found on c-fos, BDNF (brain-derived neurotrophic factor..)
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GRB2
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growth factor receptor-bound protein 2 - adaptor protein (SH2 and SH3 domain)
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mechanism of serine-threonine receptor kinases
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1 ligand 2 receptor homodimerization and cross-phosphorylation (activation) 3 activate Ras (via GRB2 and SOS)
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PKA phosphorylate
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1 glycogen phosphorylase kinase (activate) 2 pyruvate kinase (inactivate) 3 glycogen synthase (inactivate) 4 CREB protein
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PKC, effect - phosphorylate
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1 Raf kinase 2 membrane receptors (cause receptor internalization) 3 other membrane proteins (Ca2+ ATPase, Na+/H+ exchanger)
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PKC, origin of name, classification
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Ca2+-dependent, family (10 isoenzymes), 3 classes - 1 conventional/classic (Ca2+, DAG, PL) 2 novel (DAG) 3 atypical (neither DAG or Ca2+)
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Ras protein (RAt Sarcoma)
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monomerig GTPase, help to relay signals (first discovered in viral gene causing rat sarcoma)
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Ras superfamily
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large superfamily of monomeric GTPases/small GTP-binding proteins, Ras is the prototypical member
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receptor kinases - structure, types (ie)
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1 membrane-spanning alpha helix, dimerize when bound to ligand and phosphorylate each other, tyrosine kinases (EGFR, FGFR), serine-threonine kinases (TGF-BR)
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SOS (Sons of sevenless) protein
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guanine nucleotide exchange factor - activate Ras
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calmodulin, function and structure
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dumbbell shape, each globular end has 2 Ca2+ binding domains, when Ca2+ binds it alter the conformation so it ''wraps'' around its target proteins (ie CaM-kinase)
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cAMP and caffeine
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caffeine inhibit cAMP phosphodiesterase - partly explains its stimulatory effect
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cAMP, brain-related effects
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1 hypothalamus - increased somatostatin 2 neurons - proteins involved in long-term memory
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cholera toxin, effect in the cells
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inhibit GTP hydrolysis by alpha subunit of G protein = continuous activation (can cause diarrhea by continuous open Cl- channel)
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concentration of Ca2+ in cytosol of an unstimulated cell?
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10-7 M
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curare, related to which signal substance, which receptor
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Ach, block Ach-activated ion-channel-linked R (block neuromuscular junction)
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Delta, what
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transmembrane protein that works as a ligand for contact-dependent signaling, it inhibits neighboring cells from becoming specialized in the same way as the signaling cell (ie neurons)
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G protein - activate/do
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1 regulate ion channels (Ach on cardiomyocytes activate Gi protein, betagamma open K+ channel and hyperpolarize it) 2 activate membrane-bound enzymes (adenylyl cyclase, PLC)
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morphine and heroin, mimic which signal molecule, what receptor action
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endorphins and enkephalins (''endogenous opiates''), stimulat G-protein-linked opiate receptors
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NO - action in cell
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activate guanylyl cyclase, cGMP casue vasodilation
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retrotransposons - in which cells? 2 most frequent types? (size, contain reverse transcriptase, disease-association)
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only eucaryotes, L1 (Line-1) (have RTase, 15% of human genome, haemophilia A), Alu (11% of human genome, no RTase)
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signal transduction, u by
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message is converted from one form to another, receptors
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signaling cascades - functions
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1 transduce 2 relay 3 amplify 4 distribute/diverge 5 modulate
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TGF-B, function
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inhibit cell prolifeartion, stimulate ECM production
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valium and barbiturates, mimic which signal molecule, which receptor
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GABA, stimulate GABA-activated ion-channel-linked R
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actin filament cell junctions
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1 tight junctions/zonula occludens 2 zonula adherens 3 focal adhesions
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communicating junctions
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1 gap junctions 2 chemical synapses 3 plasmodesmata (only plants)
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Ets
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one of the largest families of transcription factors, involved in 1 cellular differentiation 2 cell cycle control 3 cell migration 4 cell proliferation 5 apoptosis 6 angiogenesis
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IFN-alpha/leukocyte interferon and IFN-beta/fibroblast interferon
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made by virus-induced leukocyte or fibroblast, 1 suppress cell proliferation 2 inhibit viral proliferation 3 enhance phagocytic activity
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intermediate filament junctions
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1 desmosome 2 hemidesmosome (half-cell, half ECM)
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JAK (Janus kinases) kinases - mechanism
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Jak kinase activate STAT (signal transducers and activators of transcription) proteins, STAT travel to uncleus and regulate gene expression
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MAPK, effect
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(a) Elk-1 -> Elk-1 (transcription factor, belong to Ets) + SRF -> ↑c-fos -> fos+jun -> ↑AP-1
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Na+/H+ exchanger/antiporter, effect
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alkalize cell, alkalization stimulate DNA synthesis (pH below 7.2 inhibit DNA synthesis)
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receptors associated w kinases - ligands?
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cytokines, prolactin
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receptors associated w kinases - types
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1 Src kinase family (Src, Lck, Yes) (EGFR, PDGFR) 2 Jak kinases (IFN-γ/alpha/betaR)
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Src kinases - mechanism
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1 src 2 SHC (adaptor protein) 3 GRB2 4 SOS 5 Ras 6 Raf..
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SRF, full name, what?
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serum response factor/c-fos serum response element-binding transcription factor, bind to SRE in promoter region of target genes (many immediate early genes)
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AP-1 (activator protein 1)
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transcription factor, dimer of fos and jun (control differentiation, proliferation, apoptosis) (stimulated by cytokines, GFs, stress, infection..)
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cytokinesis starts during
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anaphase
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difference between cell in G0 and cell in cell cycle
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cell in Go need to ''prepare'' and use longer time before it can proliferate according to signal
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early response genes, which protein is frequently involved
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general term used to describe genes rapidly and transiently expressed by cells wi 0.5-2h in response to environmental stimuli (we suppose that they are already produced and only needs activation (posttranslation)), AP-1 is frequently involved
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early response genes/third messengers, function
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multiply and propagate the initial (gene activation) process by activating delayed-early response/late response/secondary response genes, also self-activating
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ERG - type of compounds
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1 protein kinases (tyrosine mostly) 2 cytokines 3 receptors (cytokine, GF) 4 cytoskeletal proteins 5 ECM components 6 competence factors
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Immediate early genes (IEGs), ie
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response mechanism that is activated at the transcription level in the 1st round of response to stimuli before any proteins are synthesized (early regulators of cell growth and differentiation signals, ''gateway to genomic response'', c-fos, c-myc, c-jun (most are transcription factors and DNA-binding proteins), transcriptional activators and repressor subset of early response genes
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M phase of cell cycle
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mitosis, cytokinesis
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mechanisms of cytokinesis
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1 animal cell = contractile ring 2 plants = phragmoplast (growth from center to edges of cell wall) 3 algae, fungi = plasma membrane invagination
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normal somatic cell cycle
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24h
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prometaphase
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1 disintegration of nuclear envelope (lamin phosphorylation) 2 microtubules attach to kinetochore
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prophase
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1 chromosome condensation 2 two sister chromatids
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signal for proliferation for cell in GO
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myc protein
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subcycles of cell cycle
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1 DNA synthesis cycle 2 Nuclear division cycle 3 growth cycle 4 cell division cycle
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telophase
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1 reintegration of nuclear envelop (dephosphorylation of lamins)
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APC, full name, activated by? effect?
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anaphase promoting complex, M-Cdk/cyclin B-Cdk1, ubiquitinate m-cdk for proteolysis and facilitate physical separation of replicates chromosomes in anaphase
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CAK, full name, what?
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CDK-activating kinase/CDK7+cyclin H, activate CDK(1,2,4)
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cdk activators
|
1 CAK 2 cdc25 phosphatase (Cdk1 - mitosis)
|
|
|
CDK inhibitors
|
1 CKI\p21 (G1->S, inhibit Cyclin E\CDK2) 2 Wee1 gene\Wee1-like kinase (G2->M, inhibit cdc2(cell division control protein 2)\CDK1) 3 P16 (inhibit G1-Cdk, tumor suppressor)
|
|
|
CDK-cyclin complex - effect
|
phosphorylate other proteins, which lead to microtubule formation and chromatin remodeling
|
|
|
CDKs, what type of kinases?
|
serine-threonine kinases
|
|
|
CKI, full name, what?
|
CDK inhibitor protein, bind and inhibit cyclin/CDK (pri for G1 and S phase)
|
|
|
Competence fators
|
G0 to G1
|
|
|
cyclin CDK for entry to S phase
|
cyclin E/CDK2 / S-Cdk (favorable environment, not damaged DNA?)
|
|
|
cyclin/CDK for entry into mitosis
|
cyclin B/CDK1 /M-Cdk (is all DNA replicated? DNA not damaged? is environment favorable?)
|
|
|
hep B virus can cause
|
hepatocellular carcinoma
|
|
|
positive feedback loop of Rb
|
1 CDK2-cyclin E phosphorylate Rb 2 rb is inactive 3 E2F can upregulate expression of CDK2-cyclin E
|
|
|
regulation of cdk1 (mitosis)
|
+ B cyclin, activating kinase, activating phosphatase, - inhibitory kinase
|
|
|
RNA viruses require which enzyme to replicate?
|
RNA-dependent RNA polymerase
|
|
|
structure of virion
|
1 nucleic acid/genophore 2 capsid (3 outer envelope - enveloped viruses)
|
|
|
virus, size
|
25-400 nm
|
|
|
+ssRNA
|
= mRNA, don't need RNA polymerase packaged into the virion
|
|
|
-ssRNA
|
complementary to mRNA/=template strand, must be converted to +RNA/mRNA by RNA-dependent RNA polymerase prior to translation
|
|
|
capsid, structure
|
subunits of capsomers (u identical, can be made of several proteins), capsid = quaternary structure of capsomere
|
|
|
enveloped viruses
|
1 herpesv 2 poxv 3 flaviv 4 togav 5 filov 6 orthomyxov 7 paramyxov 8 retrov
|
|
|
lysogeny
|
viral genome is incorporated into the genome of the host cell (as a provirus or prophage/probacteriophage and replicated together with it
|
|
|
monocistronic and polycistronic transcripts
|
mono - 1 promoter = 1 functional protein, poly - 1 promoter = more than one functional protein
|
|
|
outer envelope of virus, derived from
|
lipid layer from host cell, glycoproteins (HIV can react w CD4 on T-helper) coded by viral genes
|
|
|
proteins of viruses
|
1 structural (capsid) 2 enzymes - viral reproduction 3 proteins that facilitate the virus' release from the cell 4 proteins that influence the synthesis of proteins of a host cell, so it becomes permissive for viral reproduction
|
|
|
repair mechanisms in RNA virus?
|
No
|
|
|
reproductive/lytic cycle
|
virus is multiplied wi the cell and virions are released, u accompanied by cell disintegration
|
|
|
reproductive/lytic cycle, steps
|
1 adsorption of virion on cell surface and its penetration into the cell 2 reproduction of virion wi the cell 3 release of virions from the cell
|
|
|
size of viral genome
|
3-150 genes
|
|
|
typical structure of a viral gene (A, B1, B2)
|
A = promoter, B1 = early genes (replication machinery, cell-repressing proteins..), B2 = late proteins (structural)
|
|
|
virus - morphology
|
1 regular polyhedral (eicosahedral (20 triangular faces, 12 vertices), spherical) 2 helical cylinder (Rod-shaped) 3 specific shape of bacteriophages (head, tail, filaments)
|
|
|
viruses that easily combine genetic information w other viruses u have which type of genophore?
|
fragmented viral genome
|
|
|
animal viruses
|
zooviruses
|
|
|
baltimore, classes
|
1 dsDNA (adeno, papova, pox, herpes) 2 ssDNA (parvo) 3 dsRNA (reo, rota) 4 +ssRNA (picornavirus)
|
|
|
classification of virus
|
1 disease 2 type of host cell 3 structural 4 genophore 5 baltimore classification (method of mRNA synthesis)
|
|
|
hepatitis virus
|
hep A = picornaV, hep B = hepadnaviridae, C = flaviviridae
|
|
|
herpesvirus, types
|
1 herpes simplex 1 virus/herpes facialis/labialis 2 varicella-zoster virus (chickenpox) 3 Epstein-barr virus (infectious mononucleosis (kissing virus), Burkitt's lymphoma)
|
|
|
interaction virus-cell
|
1 death of the cell 2 cytopathic effect (damage of any funciton of the cell, can be reversible) 3 wo cell damage 4 slow viruses (don't damage cell but change some characteristics (ie structure of plasma membrane), degenerative NS disease?)
|
|
|
mechanisms of viral penetration into the cell
|
1 fusion of outer envelope w plasma membrane 2 receptor-mediated endocytosis 3 bacteriophages inject their genophore
|
|
|
orthomyxovirus, types
|
1 influenza virus A (man, birds, pigs) 2 influenza virus B (man) 3 influenza virus C (human, pig, lack neuraminidase (other influenza virus use neuraminidase for off-budding)
|
|
|
papovavirus - types
|
1 papillomavirus (cervical carcinoma) 2 polyomavirus (polyoma for rodents)
|
|
|
plant virus
|
phytovirus (tobacco mosaic v)
|
|
|
release of virions from the cell, mechanisms
|
1 lysis of the cell (bacteriophage = lytic enzymes, autolytic process of damaged cell) 2 exocytosis
|
|
|
respiratory viruses
|
1 respiratory syncytial virus/RSV (paramyxoV), adenovirus, influenza
|
|
|
transmission of viruses
|
1 horizontal transmission (direct viral transmission form host to host) 2 vertical transmission (host parent to host progeny) 3 host to host via vector (ie insect)
|
|
|
virus of fungi
|
mycovirus
|
|
|
ATR, full name, what
|
Ataxia Telangiectasia and Rad3 related protein - tumor suppressor, protein kinase activated by DNA damage that initiate a cascade that cause cell cycle arrest
|
|
|
binary fission, difference from mitotic division+cytokinesis
|
binary fission cannot be divided into pro-, meta-, ana- and telophase because prokaryotes don't have nucleus and centrosomes (chromosome attach directly to cell membrane before cell division)
|
|
|
cytotoxic agents, what, ie (3)
|
A substance that inhibit or prevent the functions of the cell, cause destruction of cells or both, ie 1 methotrexate (folic acid antagonist) 2 doxorubicin (antibiotic, intercalate dsDNA) 3 Cyclophosphamide (alkylating agent = induce apoptosis by being mutagenic)
|
|
|
IRP - full name, what
|
iron regulatory protein, proteins that can bind to iron response elements (IRE) and affect mRNA translation thereby regulating the synthesis of specific proteins
|
|
|
protein kinase A, synonym
|
cAMP-dependent protein kinase
|
|
|
role of special adenine nucleotide of intron
|
makes lariat loop (linkage of 5' end of intron to 2'OH group of its ribose)
|
|
|
secondary genes, ie
|
effector genes of the cell cycle, 1 cyclins 2 CDKs 3 p53
|
|
|
spiral shaped bacteria, types, ie
|
1 vibrio (S-/comma-shaped, very motile/vibrating, cholera) 2 spirillum (spiral, large) 3 spirochete (spiral, smaller)
|
|
|
the two most frequent spontaneous chemical reactions known to create serious DNA damage in cells
|
1 depurination (remove purine, = deletion of nucleotide pair) 2 deamination (C to U)
|
|
|
vacuoles (plant structure), function
|
storage (nutrients, waste products), degradative compartment, control against swelling
|
|
|
virus can induce cell death by
|
1 degenerative processes wi the cell (ie irreversible block of DNA transcription) 2 active lysis by lytic enzymes (bacteriophage) 3 apoptosis induction
|
|
|
why can primase begin new polynucleotide chains?
|
because it don't proofread its work
|
|
|
Cadherins - found in which intercellular junctions? origin of name?
|
adherent junctions (actin) and desmosomes (intermediate filament), Ca+ dependent
|
|
|
CaM-kinase, origin of name, function
|
Ca2+/Calmodulin-dependent protein kinase, myosin-light chain kinase (MLCK) - contraction of smooth muscle, multifunctional CaM-kinase/CaM-kinase II = involved in long-term potentiation of CNS (1-2% of proteins in CNS)
|
|
|
G proteins - types
|
1 Gs (activate adenylyl cyclase, ie adrenalin, glucagon, LH, PTH, ACTH) 2 Gi (regulate ion channels, inhibit adenylyl cyclase, ie somatostatin) 3 Golf (olfactory - smell) 4 Gt (transducin - visual) 5 Gq (activate PLC)
|
|
|
Gi/inhibiting adenylyl cyclase, associated receptors
|
1 acetylcholine M2 and M4 R 2 alpha 2a-c adrenergic R 3 histamine H3-4 R
|
|
|
GPCRs and signaling pathways, association w drugs
|
a 50% of all known drugs work on it
|
|
|
Gs/adenylyl cyclase - associated receptors
|
1 5-HT (type H4 and H7) serotonergic R 2 ACTH R 3 calcitonin R 4 CTRH R 5 glucagon R 6 beta-adrenergic R (beta1-3)
|
|
|
MAP-kinase - origin of name
|
Mitogen-Activated Protein kinase
|
|
|
matrix protease, what, associated w
|
enzyme that cleave extracellular proteins, used by macrophages to invade, pathology - cancer metastasis, arthritis (breakdown of cartilage)
|
|
|
nerve growth factor (NGF), receptor, effect
|
RTK, survival factor for developing neurons
|
|
|
nitric oxide, structure
|
O=N* (radical)
|
|
|
PDGF (platelet-derived growth factor), receptor, effect
|
RTK, mediate cell proliferation in wound healing
|
|
|
phosphatidyl-inositol 3-kinase (PI 3-kinase), activated by? activates?
|
RTKs, acitvate inositol PLs (PI(3,4,5)P3) in the membrane, these become docking sites for signaling proteins - PDK1 (can also directly activate target proteins) activate protein kinase B (PKB)/ATK (serine-threonine kinase), PKB is involved in signalling cells to grow and survive (survive by inhibiting BH3-only proteins)
|
|
|
procollagen proteinase
|
extracellular enzyme that catalyze removal of terminal domains (pro) of procollagen
|
|
|
Ras protein, mutation in how many cancers?
|
a 30%
|
|
|
receptor serine threonine kinases, associated ligands, effect
|
TGF-B superfamily, phosphorylate and activate SMADs (gene regulatory proteins) (involved in development)
|
|
|
IAPs (inhibitiors of apoptosis) - ie
|
Smac/Diablo, Omi (have BIR (baculovirus IAP repeat) domains, controversial role)
|
|
|
is G0 part of the cell cycle?
|
No
|
|
|
link between intrinsic and extrinsic apoptotic pathways
|
BH3 protein Bid (caspase-8 cleave/activate Bid = tBid, tBid translocates to mitochondria and inhibit Bcl2 proper)
|
|
|
M - phases, mitosis - phases
|
1 Preprophase 2 Prophase 3 Prometaphase 4 Metaphase 5 Anaphase 6 Telophase 7 Cytokinesis, same - 7
|
|
|
Picornavirus, of which group? types?
|
+ssRNA, 1 poliov 2 hep A 3 rhinov
|
|
|
second messengers
|
1 cAMP 2 IP3 3 DAG 4 Arachidonic acid 5 cGMP
|
|
|
shape of RNA in virus
|
linear ss or ds
|
|
|
signal substance causing cells between developing fingers and toes to kill themselves
|
bone morphogenic protins (BMPs)
|
|
|
spontaneous mutations wo influence of mutagens occur at a rate of x/gene/cell division, how many mutations is thus a gene likely to have over a lifetime?
|
10-6-10-7/gene/cell cycle, 109/gene
|
|
|
survival factors - intracellular mechanism
|
increase Bcl2 (proper, xl), inhibit BH3-only proteins
|
|
|
Trk receptor, what, function, class
|
family of RTKs, involved in regulating neuronal survival and differentiation (plasticity), classes - TrKA (nerve growth factor), TrkB (BDNF - growth and survival factor for neurons)
|
|
|
TrkA/High affinity NGFR/Neurotrophic tyrosine kinase type 1, oncogene?
|
No
|
|
|
viruses that mutates the most?
|
segmented RNA vrius
|
|
|
what determines the sensitivity of an animal cell to apoptosis-inducing stimuli?
|
Bcl2, IAPs (inhibitors of apoptosis), anti-IAPS (IAPS and anti.. are controversial - inactivation in mouse cause no apparent change, active in drosophila, viral origin?)
|
|
|
which viruses have point mutations of 10-4?
|
RNA viruses
|
|
|
3 principles for creating structural organization of tissue
|
1 cell communication 2 selective cell-cell adhesion 3 cell memory
|
|
|
activation of initiator procaspases
|
caspase recruitment domain (CARD) enable them to assemble w adaptor proteins into activation complexes where they can cleave/activate each other
|
|
|
APC gene, full name, what
|
adenomatous polypoisis coli gene, tumor suppressor gene (inhibit beta-catenin of Wnt (mutation = wingless phenotype) pathway, signaling pathway for proliferation)
|
|
|
Appx duration of cell cycle in hepatocytes
|
1 year
|
|
|
Appx duration of cell cycle of early frog embryo
|
30 minutes (basically omit G1 and G2 and go from S to M)
|
|
|
Appx duration of cell cycle of intestinal epithelial cells?
|
12h
|
|
|
Appx duration of cell cycle of mammalian fibroblasts i culture
|
20 hours
|
|
|
catalytic histochemistry - used enzyme? for which techniques? (3)
|
Horseradish peroxidase (product is fluorophor) - used in western blotting, immunohistochemistry and ELISA
|
|
|
change in plasma membrane during apoptosis
|
negatively charged phosphatidylserine is ''flipped'' to the outside - marker for phagocytosis, block inflammation
|
|
|
chaperonin and molecular chaperons
|
chaperonin (barrel-shaped), molecular chaperones (free, ie HSP (40, 70)
|
|
|
DAPI
|
fluorescent stain that binds strongly to DNA, blue emission
|
|
|
deprivation of extracellular survival signals - mechanism for apoptosis
|
Map kinase (JNK) upregulate transcription of BH3 protein (Bim) - trigger intrinsic pathway
|
|
|
Fast growing cell which has a cell cycle duration of 24h, duration of 1 G1 2 S 3 G2 4 M. Variation of phases
|
1 10h, Longest and most varied because cell can enter G0 2 5-6h, quite constant 3 3-4h, quite variable 4 2h
|
|
|
Gleevec
|
protein that inhibit a tyrosine kinase oncogene of chronic myeloid leukemia (CML) by binding to its ATP-binding site
|
|
|
how does p53 trigger apoptosis
|
activate transcription of BH3 proteins Puma and Noxa (proapoptotic Bcl2)
|
|
|
Immunohistochemistry
|
based on antibody-antigen + marker
|
|
|
difference between hnRNA and mRNA
|
hnRNA = the initial transcript, mRNA = capped and tailed transcript
|
|
|
enhancer, what, location
|
DNA stretch that alters gene expression by binding to transcription factors, can be located close/far from/within (intron) of the gene who it regulates
|
|
|
hnRNA
|
heterogenous nuclear RNA, the initial RNA transcript
|
|
|
mischarged tRNA
|
bound to wrong AA
|
|
|
what are the four features of the genetic code?
|
1 unambiguous (1 codon specify one aa) 2 degenerate (more than one codon can code for same aa) 3 commaless (non-overlapping, e = virus) 4 universal (e = mitochondria, archae, mycoplasma, some yeasts)
|
|
|
what does the P in the P-site stand for? A in A-site?
|
P = peptidyl (parked), A = aminoacyl (afferent)
|
|
|
what enzyme is responsible for ''charging'' tRNA? mechanism?
|
aminoacyl-tRNA synthetase, via ATP (the energy of the bond is further used to create peptide bond)
|
|
|
what is the function of DNA polymerase during DNA replication?
|
1 5'-3' exonuclease acticity of DNA polymerase I degrades RNA primer 2 3'-5' exonuclease activity proofreads each added nucleotide 3 dna polymerization
|
|
|
what is the function of DNA topoisomerase during DNA replication?
|
create a nick in the helix to relieve supercoils
|
|
|
what is the function of RNA polymerase I?
|
make rRNA
|
|
|
what is the function of RNA polymerase II?
|
make mRNA
|
|
|
what is the function of RNA polymerase III?
|
make tRNA and some small RNA
|
|
|
what is the mRNA initiation codon?
|
AUG, rarely GUG
|
|
|
what is the mRNA stop codons?
|
1 UGA (u go away) 2 UAA (u are away) 3 UAG (u are gone)
|
|
|
what prevents an incorrect AA-tRNA pairing?
|
if incorrect, the AA-tRNA bond is hydrolyzed by aminoacyl-tRNA synthetase
|
|
|
# of cell types in human
|
a 200
|
|
|
antibiotics - mechanisms
|
1 integrase inhibitors 2 RT inhibitors (azidothymidine for HIV) 3 fusion/entry inhibitors 4 protease inhibitors (HIV proteases - needed for viral maturation) 5 replication inhibitors 6 inhibition of releasing of viruses
|
|
|
cell determination, what? determined or specialized first?
|
process by which the cell becomes committed to a certain specialization/differentiation, determination
|
|
|
does all cells contain actin?
|
no - not prokaryotes
|
|
|
how do you do a PCR?
|
1 denature DNA by heat 2 cool DNA and let the primers anneal 3 heat-stable polymerase replicates DNA following each primer 4 repeat
|
|
|
how do you do a southern blot?
|
1 electrophorese DNA on a gel 2 transfer to a filter (blotting) 3 denature the DNA 4 expose to a labeled DNA probe 4 visualize probe annealed to desired DNA fragment
|
|
|
lamins, what happends when they're phosphorylated?
|
intermediate filaments of nuclear lamina, dissociates
|
|
|
microtubules, subunits, create
|
alpha+beta tubulin, mitotic spindle and flagellum (9+2)
|
|
|
microvilli is created by which cytoskeletal structure?
|
microfilaments (actin)
|
|
|
nucleolus, function
|
RNA production
|
|
|
ribosome, structure
|
small and large subunit of proteins and rRNAs (3 types)
|
|
|
vimentin
|
intermediate filament of CT
|
|
|
what is the smallest type of RNA?
|
tRNA (tiny)
|
|
|
which eucaryotic cells have rigid cell wall, material?
|
1 plants 2 fungi 3 algae, cellulose in plants
|
|
|
which is the most abundant type of RNA?
|
rRNA
|
|
|
2 types of tissue repair
|
repair regeneration (replacement by same cells), wound healing (scar tissue formation, fibroblasts, PDGF)
|
|
|
cell memory
|
cells ability to remain differentiated after the original signal responsible has disappeared (possibly via positive self-activation feedback)
|
|
|
cytokine, what, classification, types
|
Signal peptide/protein that regulate intensity and duration of immune response, types = interferons, interleukins, lymphokines, can be endocrine, paracrine and autocrine
|
|
|
evocator/inductor
|
a factor in the control of morphogenesis
|
|
|
gene regulatory protein/transcription factor
|
a substance that binds to a specific DNA sequence to influence the transcription of a gene
|
|
|
Hedgehog protein
|
secreted signal protein, proto-oncogene, many roles involving cell differentiation and gene expression in embryos and adult tissue (regulated wia Hedgehog signalling pathway, Gli protein in nucleus)
|
|
|
HOM/Hox, what?
|
HOM = drosophila, Hox = higher animals
|
|
|
Homeodomain
|
DNA-binding motif that define the Hox gene complex, apx 60 nucleotides
|
|
|
Hox gene complex
|
cluster of genes (13) coding for gene regulatory factors, each gene has a homeodomain and specify anterior-posterior body axis (mainly) and limb development, 4 homologous complex (Hom, on different chromosomes), but no complex have all genes
|
|
|
induction
|
the influence exerted by an organizer/evocator on the differentiation of adjacent cells or on the development of an embryonic structure
|
|
|
mechanisms controlling differentiation
|
1 asymmetry (chemical assymetry in egg) 2 embryonic induction 3 positional signals 4 intracellular clock (cells are spontaneously changing their internal environment during time)
|
|
|
morphogen, ie (5)
|
signaling molecule that acts on cells to produce specific cellular responses dependent on morphogen concentration, ie TGFbeta, Hedgehog, Wnt, EGF, FGF
|
|
|
morphogenesis
|
differentiation of cells and tissue in the early embryo that establishes the form and structure of the various organs and parts of the body
|
|
|
positional information in relation to cell differentiation
|
cells are able to get information reflecting their location in the body due to concentration gradients
|
|
|
Wnt protein
|
can have many different roles in controlling cell differentiation, proliferation and gene expression in embryo and adult tissue, secreted signal protein, proto-oncogene (mediated via beta-catenin and TCF (gene regulatory protein, must complex w beta-catenin to be active))
|
|
|
apoptosis, involvement
|
1 cell elimination (damaged cells) 2 tissue homeostasis 3 non-needed cells (developing neurons competing for survival factor) 4 forming during embryogenesis 5 immune system 6 pathology
|
|
|
caspases, derivation of name, structure, structural change w activation
|
Cysteine (cleavers)-ASPartic (cleavees) proteASES, tetramer (2 small+2 large), prodomain of procaspase is removed
|
|
|
cell senescence
|
a phenomenon where after a certain number of cell divisions the cell lose its ability to proliferate and finally inevitably dies
|
|
|
Cell senescence, cause, mechanism
|
telomere, DNA damage due to shortening of telomere -> p53 -> p21 /apoptosis -> (inhibit)cyclin E/CDK2 -> block progression to S-phase
|
|
|
Hayflick limit, for what? how many?
|
human embryonic cells, 50
|
|
|
homeobox
|
a short (180bps) conserved DNA sequence that encodes a DNA-binding motif (homeodomain)
|
|
|
homeotic mutation
|
mutation that cause cells in one region to behave as though they were located in another
|
|
|
multipotent stem cells
|
stem cells of adult organisms, can differentiate to a family of cells (ie hematopoietic)
|
|
|
necrosis
|
pathological cell death due to irreversible cell damage resulting from exposure to extreme non-physiological conditions (heat, radioactivity, hypoxia, toxic substances)
|
|
|
necrosis vs apoptosis
|
1 passive / active 2 intact DNA / DNA degradation 3 plasma membrane disintegration / intact (apoptic bodies) 4 inflammatory resp / no 5 cell swelling / cell shrinking 6 intact chromatin / chromatin condensation
|
|
|
pathology related to increased apoptosis
|
1 AIDS (helper T cells) 2 Alzheimer's (cortex, amygdala) 3 Parkinson's (basal ganglia, dopamine) 4 amyotrophic lateral sclerosis (ALS) (motor neurons in brain and spinal cord) 5 ischemia (reperfusion injury by increased ROS) 6 toxin-induced liver disease (alcohol) 7 myelodysplastic syn/preleukemia
|
|
|
pathology related to inhibited apoptosis
|
1 cancer (p53, hormonal (breast, prostate, ovarian)) 2 autoimmune - systemic lupus erythematosus (SLE) (vs connective tissue)
|
|
|
physiological cell renewal, types
|
1 proliferation of differentiated cells (hepatocytes, endothelial) 2 renewal from undifferentiated stem cells (epidermis (unipotency), blood cells (multipotent))
|
|
|
pluripotent stem cell
|
embryoblast and embryonic stem cell (cannot form placenta)
|
|
|
relenza and tamiflu, mechanism
|
neuraminidase/sialic acid inhibitors - sialic acid assist viruses in budding off = prevent virus from being released
|
|
|
totipotent stem cell
|
can give rise to every cell type, from zygote before morula stage
|
|
|
Apoptosis inducing factor (AIF)
|
normally found in intermembrane compartment of mitochondria. 1 caspase-independent effect = protein degradation, chromatin condensation 2 regulate mitochondrial membrane permeability via Cyt-c+casp9
|
|
|
apoptosome
|
heptamer of apaf1 (apoptotic protease activating factor-1), formation/oligomerization is caused by cyt C (w hydrolysis of dATP), recruit procaspase 9 which are activated by proximity in the apoptosome
|
|
|
apoptotic signal molecules
|
1 glucocorticoids (glucose, cortex, steroid) (ie T cells, proinflammatory proteins) 2 cytokines - survival factors (IL3-5, GM-CSF, IGF1) 3 ligands of receptors (death receptors) w death domain (TNF, FAS) 4 granzyme B (perforins)
|
|
|
Baltimore virus classification, 4-7
|
4 +ssRNA (picorna, corona, flavi, toga(encephalitis v, rubella)) 5 -ssRNA (rhabdo (rabies), paramyxo (measles), orthomyxo, filo (ebola)) 6 ssRNA + RT (retro, lenti) 7 dsDNA + RT (hepadne (hep B))
|
|
|
Bcl-2 (B-cell lymphoma), what?
|
family, mitochondrial membrane proteins (govern permeability), (have bcl-2 homology (BH) domain, 1-4) 2 types - antiapoptotic (BH1-4) (bcl2-proper, Bcl-xl) proapoptotic (BH123 - bax, bak), (BH3), make dimers (ratio of pro/anti = outcome)
|
|
|
Bcl-2, mechanism
|
regulate release of cytochrome C and other mitochondrial proteins from the intermembrane space
|
|
|
Caspases, classification
|
1 initiators (#8-10) 2 executioner (#3,6,7) 3 Inflammatory (#1/ICE (interleukin-1 converting enzyme), 4,5))
|
|
|
cytochrome C
|
heme protein, released from mitochondria by increased Ca2+ (cause positive feedback cycle by releasing Ca2+ from ER), activate caspase 9
|
|
|
E2F protein
|
gene regulatory proteins that switch on many genes that encode proteins required for entry into S phase (cyclins, CDKs, DNA repair protein), family (some are activators (1-3A), suppressors (3B-8) (only 3 are A and B))
|
|
|
executioner caspases activate
|
death substrates
|
|
|
FAS ligand, activation
|
transmembrane protein, TNF family, trimer of FASL-FASR = activation, FASR form DISC
|
|
|
GM-CSF, full name
|
granulocyte macrophage colony stimulating factor
|
|
|
main ligand-receptor for apoptosis induction in the immune system, actions
|
FAS-Fas receptor, 1 T-cell homeostasis 2 CD8 T-cell activity (FAS-perforin) 3 immune privilege (cornea, fetus..use to kill lymphocytes) 4 tumor counterattact (increased fas)
|
|
|
main step of activation of apoptosis is changes in permeability of mitochondrial menbrane, releasing cytochrome C, this can be triggered by
|
1 PT (permeability transition pore) (by increased Ca2+, ROS) 2 Bcl-2 proaptotic dimers
|
|
|
p53, activated by, cause
|
DNA damage -> ↑p53 -> ↑p21 (inhibit CDK2\cyclin E), ↑Bax (proapoptotic member of Blc-2)
|
|
|
Poly ADP-ribose polymerase (PARP)
|
family, repair single-strand DNA nicks (caspase cause DNA cleavage, PARP use ATP = ATP depletion)(induce apoptosis directly through PAR which stimulate mitochondria to release AIF)
|
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|
Rb protein
|
tumor suppressor, regulate cell cycle by binding to and inhibiting E2F1 (=block progression to S phase)
|
|
|
carcinogenesis - theory of immune surveillance
|
carcinogenesis due to error of immune system
|
|
|
carcinogenic viruses
|
oncogenic RNA viruses (retroviruses), oncogenic DNA viruses (3)
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|
carcinogens
|
1 chemical 2 physical 3 viruses
|
|
|
chemical carcinogens - types, u cause
|
1 aromatic hydrocarbons (enzymatically changed to carcinogenic epoxides in the body) (aflatoxin) 2 nitrosamines (nitrates, nitrites) 3 acridine dyes, point mutations
|
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|
death substrates
|
1 caspase-activated DNAse (DNA fragmentation (endonuclease)(really degrade a binding/inactivating protein) 2 Poly ADP-ribose polymerase (PARP) 3 structural proteins (lamins, cytoskeletal proteins, cell adhesion proteins) 4 regulatory proteins (Rb)
|
|
|
DISC, full name, what?
|
Death inducing signaling complex, FasR+FADD(Fas-associated protein w death domain - adaptor)+caspase 8
|
|
|
functional group of oncogenes
|
1 growth factors (v-sis (PDGF part)) 2 receptor tyrosine kinases (v-erbB (EGF receptor) 3 non-receptor tyrosine kinases (v-src (src kinase)) 4 G-proteins (v-Hras (Ras protein)) 5 Serine-threonine kinases (v-raf (Raf-1 kinase) 6 Transcription factors (v-fos, v-myb, v-myc) 7 factors controlling apoptosis (bcl-2 proper)
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|
|
only bacterium linked to cancer, mechanism, why not treat it?
|
helicobacteri pylori (live above mucosa layer of stomach, protected from pH by urease (create ammonia from urea)), carcinogenesis linked to chronic inflammation by thinning mucosa layer, decrease risk of a type of esophageal cancer
|
|
|
physical carcinogens - types, u cause
|
non-ionizing radiation (m UV) = tautomeric changes (thymine dimers), ionizing radiation (reactive radicals - chromsomal rearrangements)
|
|
|
Rule of 2Qs of oncogenes
|
Altered quantity or altered quality
|
|
|
spontaneous transformations - mechanisms?
|
quantum mechanics - change of electron from one hydrogen base pairing ->-> mutation
|
|
|
transformed cells, characteristics
|
1 decreased dependence on survival cytokines 2 loss of anchorage dependence (BM, focal adhesions+hemidesmosomes - clone in agarose gel?) 3 loss of contact inhibition 4 immortality (telomerase) 5 invasivity 6 abnormal proliferation in space and time 7 clonal 8 multistage process 9 inability to differentiate 10 resistant to apoptosis 11 genetic instability
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|
|
virus of hepednavirus family linked to cancer, which cancer
|
hepatitis B virus - hepatocellular carcinoma
|
|
|
virus of herpesvirus family linked to cancer, which cancer
|
Epstain-barr's virus/human herpesvirus 4(HH4) - Burkitt's lymphoma (B-cell), nasopharyngeal carcinoma (also cause infectious mononucleosis) (linked to chronic fatigue syn and MS)
|
|
|
virus of papovavirus family linked to cancer, which cancer
|
Papillomavirus - carcinoma of uterine cervix
|
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Chemotherapy
|
1 cytostatica 2 cytotoxica 3 cytokines 4 monoclonal antibodies 5 gene therapy
|
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Cytochalasin
|
damage actin filaments
|
|
|
cytokines - mechanisms in cancer treatment
|
1 inhibit cell proliferation+induce apoptosis (INFs, TNF) 2 supportive effect - support immune system while under treatment (IL-2, GM-CSF)
|
|
|
cytostatic agents, what, ie
|
only react w repression machinery of cell (particularly w cell cycle, ie block mitotic spindle), vinca alkaloids (vinblastine, vincristine)
|
|
|
DNA deamination
|
cytosine to thymine
|
|
|
gene therapy of cancer
|
antisense oligonucleotides (against oncogene mRNA), transfection (working tumorsuppressor genes)
|
|
|
mdm2?
|
proto-oncogene, inhibitor of p53
|
|
|
Latrunculin
|
Binds actin subunits and prevents their polymerization
|
|
|
monoclonal antibodies, use in cancer treatment
|
1 inhibit cell proliferation 2 targeted drugs (bind to epitope of cancer cell)
|
|
|
most prevalent class of cancers, least prevalent
|
carcinomas (85%), sarcomas (2%)
|
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Phalloidin
|
bind and stabilize actin filaments/polymerization
|
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|
tumor
|
a formation made of cancer cells and normal cells controlled by them = stroma, blood vessels
|
|
|
tumor suppressor genes - ie
|
Rb, p53
|
|
|
taxol
|
bind and stabilize microtubules
|
|
|
drugs that binds tubulins (subunits) and prevents their polymerization to microtubules
|
1 colchicine 2 colcemid 3 vinblastine 4 vincristine 5 nocodazole
|
|
|
at which end of the tRNA is the aa bound?
|
covalently bound to the 3' end
|
|
|
can RNA polymerases initiate chains?
|
Yes
|
|
|
describe the main difference in eukaryotic and prokaryotic synthesis of RNA
|
eukaryotes have 3 different RNA polymerases (I-III), prokaryotes have 1
|
|
|
describe the number of bonds per purine-pyrimidine pair, which is stronger
|
CG = 3 (stronger), AT = 2
|
|
|
difference between eukaryotic, bacterial, viral and palsmid origin of replications
|
eukaryotic = multiple, bacterial/viral/plasmid = one
|
|
|
How is the original transcript processed in eukaryotes?
|
1 capping on 5' end 2 Polyadenylation on 3' end (200 AAs) 3 Splicing
|
|
|
in eukaryotes, what must occur before an newly synthesized RNA transcript leaves the nucleus?
|
only processed RNA is transported out of the nucleus of eukaryotes
|
|
|
name the charged histones around which (-) charged DNA loops (nucleosome core)
|
H2A, H2B, H3, H4
|
|
|
name the enzymes involved in ss-DNA repair
|
1 excision-specific glycolase (recognize and remove damaged base) 2 endonuclease (make a break) 3 exonuclease (remove short sequence) 4 polymerase 5 DNA ligase
|
|
|
structure of chromatin
|
condensed by (-) charged DNA looped around (+) charged histones), H1 ties nucleosomes together into a string (30nm fibers)
|
|
|
tRNA structure
|
75-90 nucleotides, cloverleaf form, anticodon end is opposite to the 3'aminoacyl end.
|
|
|
tRNA wobble
|
accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon. = Codons differing in the 3rd/wobble position may code for the same AA
|
|
|
What direction is DNA synthesized in?
|
5' to 3' (5' of incoming nucleotide bear the 3P which is the energy source for the bond, the 3' hydroxyl of the nascent chain is the target)
|
|
|
what direction is proteins transcribed in from DNA?
|
5' to 3'
|
|
|
3 end posttranslational modification of mRNA
|
1 one enzyme cut a portion of it 2 another enzyme insert a poly-A tail
|
|
|
5 end posttranslational modification of mRNA
|
capped by the addition of an atypical nucleotide of G (7-methylguanine) that is attached
|
|
|
actin is attached to integrins via
|
1 Vinculin 2 α-actinin 3 talin 4 filamin
|
|
|
annealing
|
pairing of complementary ssNAs
|
|
|
archae, characteristics
|
1 nucleosome-ish DNA 2 tRNA+rRNA gene contain intron 3 cell wall = pseudopeptidoglycan
|
|
|
ASO-PCR
|
allele-specific-oligonucleotide. target analysis. analyze a restricted area
|
|
|
beads on a string formation, what, width
|
nucleosome (histone octamer, 146 bps), 10 nm
|
|
|
blotting
|
1 molecules are separated by electrophoresis 2 transferred (blotted) to nitrocellulose membrane 3 hybridized w complementary NA probes
|
|
|
blotting, ie
|
mRNA = northern blot, DNA = southern blot, protein = western blot
|
|
|
caspases
|
proteases that mediate apoptosis
|
|
|
cause of cystic fibrosis
|
ΔF508 (deletion of Phe), on CFTR gene (cystic fibrosis transmembrane conductance regulator)
|
|
|
cDNA
|
DNA synthesized from mRNA by RT
|
|
|
cell wall on procaryotes
|
polymers of peptidoglycan/murein = N-acetylglucosamine+N-acetylmuranic acid. linked by oligopeptides
|
|
|
centrosome
|
pair of centrioles (9 triplets) at right angles, seperate chromosomes
|
|
|
Chaperones, groups
|
1 molecular chaperones 2 chaperonins (barrel structure w cavity)
|
|
|
chromatid, what, size
|
spiralization of condensed chromatin, 700 nm
|
|
|
chromatin fiber, what, width
|
nucleosome + H1, 30 nm
|
|
|
colchicine
|
stabilizes free tubulin, thus prevents formation of mitotic spindle
|
|
|
collagen, structure
|
1 preprocollagen (signal peptide) 2 procollagen (globular terminal domains) 3 collagen - 3 polymerize to form helix (called tropocollagen) 4 polymerize to form 1 fibril, further to filament
|
|
|
condensed chromatin, what, width
|
looping of chromatin fiber, 300 nm
|
|
|
CpG island
|
rich CG region, often located in promoter of housekeeping genes (frequently transcribed genes), 80% is methylated (less frequently transcribed genes)
|
|
|
desmin
|
intermediate filament of muscle cells
|
|
|
direction of proofreading of DNA polymerase
|
3' to 5'
|
|
|
DNA double helix, width
|
2 nm
|
|
|
DNA helicase
|
open DNA helix to ss for replication
|
|
|
DNA polymerase responsible for DNA repair
|
eukaryotes = beta, epsilon
|
|
|
DNA polymerase responsible for lagging strand
|
eukaryotes = alpha, prokaryotes = I
|
|
|
DNA polymerase responsible for synthesis of leading strand
|
eucaryotes = delta, prokaryotes = III
|
|
|
DNA purity
|
measured by ratio of 260 nm (DNA)/280 nm (protein) in spectrophotometry
|
|
|
DNA topoisomerases
|
unwind and wind DNA by cutting and binding DNA
|
|
|
dynein, in which structures? moves towards which end of microtubules?
|
flagella+cilia movement, move against - end on microtubule
|
|
|
error in replication machine+DNA mismatch repair system
|
one/107, one/109
|
|
|
F plasmid
|
procaryotic genes indispensable for conjugation (bacterial replication)
|
|
|
facultative anaerobic
|
can use, but don't require oxygen
|
|
|
general transcription factors
|
A large set of proteins which must assemble at the TATA box before polymerase can begin
|
|
|
genes of procaryotes
|
1000-4000
|
|
|
gram positive and negative bacteria
|
negative = murein cell wall + outer membrane (lipopolysaccharide coat), G+ contain teichoid acid as epitope
|
|
|
hemochromatosis, cause, effect
|
C282Y (cys is replaced by tyr) mutation on HFE (human hemachromatosis protein gene) affect iron metabolism
|
|
|
heterotrophs
|
require organic material
|
|
|
intermediate filament structure
|
1 helix monomer w globular domain and N and C terminal 2 coiled dimer (parallel) 3 tetramer (2 in width, one is placed in front of the other) (antiparallel) 4 two connected tetramers (2 in length, 2 in width) 5 eight tetramers twist into a round ropelike filament (in cross section)
|
|
|
junctions bound to microfilaments
|
1 adherens junctions 2 focal adhesions
|
|
|
kinesin
|
move toward + end of microtubules
|
|
|
laminin
|
trimer, +collagen IV represent main proteins of BL
|
|
|
length of human genome
|
30 000
|
|
|
major groove
|
22Å, site for transcription
|
|
|
microfilaments, function
|
1 microvilli 2 cell cortex 3 contractile ring 4 pseudopodia/lamellipodia (amoeboid movement, growth of cell processes (integrin-mediated)) 5 contractile bundle (cytokinesis (=contractile ring), muscle contraction, cell shape)
|
|
|
microtubule-organizing center (MTOC)
|
region in a cell (centrosome, basal body) from which microtubules grow
|
|
|
mRNA can be detected by
|
real-time PCR, northern blot
|
|
|
multiplex PCR
|
several pairs of primers to different sequences
|
|
|
nested PCR, advantage
|
two pairs of PCR primers are used to amplify a fragment, pair 2 bind inside the first PCR product = very specific (need error in both pairs)
|
|
|
nuclear proteins in prokaryotes
|
histone-like proteins (HLP)
|
|
|
nuclease
|
remove RNA primer
|
|
|
okazaki fragments
|
short DNA (w RNA primer on 5' end) produced on lagging strand
|
|
|
operator
|
a segment of DNA in bacteria that a repressor can bind to
|
|
|
operon
|
one transcription unit in bacteria = cluster of genes transcribed as one mRNA from one promoter (= promoter, structural genes, operator)
|
|
|
optional structures of prokaryotes
|
1 flagella 2 plasmids 3 capsule (glycocalyx)
|
|
|
plasmid
|
extrachromosomal circular dsDNA
|
|
|
plasmodesmata
|
A strand of cytoplasm that passes through openings in cell walls and connects the protoplasts of adjacent living plant cells
|
|
|
Primer
|
a segment of NA that is complementary to a given DNA sequence, and that is needed by DNA polymerase to initiate replication
|
|
|
procaryote w least amount of genes
|
mycoplasma genitalium (477)
|
|
|
prokaryotes WO cell wall
|
mycoplasma
|
|
|
promoter
|
nucleotide sequence in DNA to wich RNA polymerase bind to begin transcription
|
|
|
protamins
|
used by mature sperm cells to package DNA (as histones)
|
|
|
protein domain
|
portion of a protein that has a tertiary structure of its own, functional unit
|
|
|
proteinase K
|
release DNA from histones
|
|
|
R plasmid
|
procaryotic genes producing resistance
|
|
|
real-time PCR
|
use reverse transcriptase
|
|
|
regulatory (DNA) sequence
|
DNA sequence to which a gene regulatory protein binds to control the rte of assembly of transcriptional complex at the promoter
|
|
|
restriction fragment-length polymorphism (RFLP), principle
|
PCR product+restriction enzymes, detection through fragments of different size due to the presence or absence of mutations
|
|
|
ribosome binding sites for RNA
|
1 on small subunit for mRNA, 2-4 = large subunit. 2 = a site 3 p site (peptidyl transferase) 4 e
|
|
|
ribosomes of eukaryotes vs prokaryotes
|
prokaryotes = 70s, eukaryotes = 80s
|
|
|
rod-shaped bacteria
|
bacillus (e. coli, salmonella)
|
|
|
SDS page
|
electrophoresis type used to seperate proteins by size, unfolded by charged detergent (SDS (sodium dodecylsulfate)) and reducing agent (beta mercaptoethanol)
|
|
|
single=strand binding protein
|
clings to ssDNA and transiently keeps it from base pairing
|
|
|
sliding clamp
|
form a ring around DNA helix that binds DNA polymerase to it
|
|
|
small RNA
|
1 pre-mRNA splicing 2 transport of proteins to ER
|
|
|
snRNP (small ribonucleoproteins)
|
remove introns
|
|
|
spherical bacteria
|
streptococcus, staphylococcus
|
|
|
spirochete bacteria, shape
|
spiral
|
|
|
tautomerism, DNA relevancec
|
chemical compounds exist in 2 isomers (usually different position of H), tautomeric C can bind to A
|
|
|
telomerase
|
contain RNA, RT-activity
|
|
|
variable number tandem repeates (VNTR)
|
tandem repeat = adjacent repeats of 2+ nucleotides, VNTR = interindividual differences in # of tandem repeats
|
|
|
what is the mathematical formula for amplification in PCR
|
A=2n n=number of cycles
|
|
|
which end is usually signal sequences on proteins on?
|
N-terminal
|
|
|
why do we need to seperate transcription and translation in eukaryotes?
|
due to exon-intron constitution, would create nonsense proteins
|
|
|
BCA (bicinchoninic acid) assay method
|
peptide bond itself is responsible for color developement (562 nm, purple color detected)
|
|
|
Direct ELISA - steps
|
1 Monoclonal Ab is attached/(ab)sorbed to well (PVC-material) 2 Add suspension - Ab will bind to its cognate Ag 3 Wash out unbound antigens 4 Add similar Ab bound to reporter enzyme, which bind to immune complex 5 Wash out unbound Ab's 6 Add enzyme substrate -> color change = presence of Ag's
|
|
|
dystrophin, function, size
|
anchor to plasma membrane, 400 kDa
|
|
|
electrophoresis, separation according to
|
1 size 2 shape 3 charge
|
|
|
ELISA, full name, types
|
Enzyme-Linked Immunosorbent Assay, use ag/ab and expose it to ab/ag linked to an enzyme (direct = use antibody to detect antigen, indirect = use antigen to detect antibody)
|
|
|
FACS, full name, what
|
Fluorescence Activated Cell Sorting, a machine that can seperate and analyze cells which are labeled with fluorochrome-conjugated antibody by their fluorescence and light scatteirng patterns (differentiate cells by CD profile)(used in oncology)
|
|
|
fixative mechanism of formaldehyde/formalin
|
form crosslinking of proteins - anchors soluble proteins to the cytoskeleton
|
|
|
indirect ELISA - steps
|
1 Ag is attached/(ab)sorbed to the wall of the well (PVC material) 2 Suspension w Ab is added - form immunocomplex 3 Wash out unbound Ab's 4 Add antiantibody conjugated to reporter enzyme 5 Wash out unbound Ab's 6 Add substrate for color reaction
|
|
|
Lowry assay method
|
based on detection of tyrosine and tryptophan residues (in 500-750 nm range)
|
|
|
markers
|
1 fluorescence (fluorophor substance) 2 electron microscopy (heavy metal) 3 enzyme-linked detection (visible product, ie western blot, HRP (horse radish peroxidase) 4 radioactive substance
|
|
|
methods for desintegration/lysis of cells
|
1 mechanical (force cells through a small hole by pressure, use high frequency sound to crush cells) 2 chemical (detergent) 3 physical
|
|
|
PBS, full name, use
|
phosphate-buffered saline, fixation (w formaldehyde), washing out things from a sample
|
|
|
ultraviolet absorbance assay method
|
based on UV absorption (260-280 nm), depends on the presence of aromatic AAs (tyr, try)
|
|
|
weight of avg AA
|
110 Da
|
|
|
weight of avg nucleotide pair
|
649 Da
|
